42 Mass Profiler Professional Alignment Summary Experiment READY Export for recursion possible Total number of aligned compounds found Number of compounds found in each sample is displayed. A flag is automatically assigned to each entity in each sample: Present entity is detected and abundance measured Absent entity is not found in sample. Nominal abundance value of 1.0 is given to these. MassHunterQuant data the user can determine how flags are assigned based on input files (Present, Marginal, Absent) 15 Febrero 2011

45 Mass Profiler Professional Guided Workflow Analysis Step 3: Filter on Flags - Can be used to filter out entities which are rarely detected, therefore not very reliable - Similar to filter by frequency entities retained out of Filter on Present and Marginal (saturated entity)

47 Mass Profiler Professional Guided Workflow Analysis Step 5: QC on Samples By default, each sample is plotted according to its values for the first three Principal Components Principal Components are vectors that capture the most variance in the data. Assumption: samples within an experimental condition should be more similar to each other than to those from different conditions. Expect to see samples from the same experimental condition to group closer to each other than to samples of a different condition PCA to verify quality of Samples and separation of groups

48 PCA MassIs Profiler a Variable Professional Reduction Method PCA is a variable reduction Method PC 2 PCA to verify quality of Samples and separation of grou PC 1 An eigenvalue-eigenvector decomposition is performed on the covariance matrix of the entity expression values around zero The eigenvector corresponding to the largest eigenvalue is called the first principal component Successive principal components are eigenvectors corresponding to each smaller eigenvalue

60 Mass Profiler Professional Qualty control Goal: To remove poor quality or outlying samples before analysis Quality Control on Samples Assumption: Samples within the same experimental condition should be more similar in their global abundance profiles than samples from other experimental conditions Quality Control on Entities Goal: To remove entities which do not have reproducible measurements within a condition (%CV or SD) or entities which are rarely detected therefore not very reliable

61 Advanced Mass Profiler Analysis Professional Workflow : Analysis Analysis Tools for finding: Which entities are differentially expressed? What patterns of expression are there in the experiment? 15 Febrero 2011

62 Frequency Parametric Mass Profiler Test Professional Analysis- Parametric Test Parametric test Non- Parametric test Expression of Entity X Bell shaped distribution symmetrical about the mean MPP assume that you have sampled from populations where expression of Entity X follows a normal distribution Asymptotic Method Does not assume normal distribution Does not assume equal variances Ranks the order of normalized data across conditions for analyses With small number of replicates, nonparametric tests have less statistical power than the corresponding parametric tests P-value Calculation Methods Permutation Method

66 Mass Clustering Profiler Background Professional CLUSTERING Clustering is an unsupervised method for identifying patterns within datasets. 1) What do you want to cluster together? 2) What similarity metric to select? 3) What clustering algorithm will be applied? 15 Febrero 2011

67 Hierarchical Mass Profiler Clustering Professional Hierarchical CLUSTERING Overview: Hierarchical clustering algorithm can be used to group entities and conditions based on the similarity of their expression profiles Performing Hierarchical clustering on both entities and conditions result in a 2-dimensional dendrogram Most similar profiles are joined together into a group and groups are further joined in a tree structure until all data forms a single group 15 Febrero 2011

69 Mass Profiler Professional Pathway Analysis Pathway Anaylsis allows for Finding Biological Relevance of differencial entities Two types of pathway analysis in MPP: 1. Find Significant Pathways: Is there a significant enrichment of my entities of interest in a particular pathway? 2. Pathway Analysis: How do my entities of interest interact in a biochemical network? 15 Febrero 2011

70 Importing Mass Profiler and Professional Visualizing BioPAX Pathways Pathway Analysis BioPAX (Biological Pathway Exchange) is a standard pathway data exchange format. Pathways in the biopax format will have the extension.owl MPP users can import pathway data standard pathway sites in BioPAX level 1 or 2 format is a useful website which list repositories of pathways Databases for any organism of interest can be created using the Biopax files- Rice, zebra fish, chimpanzee, dog 15 Febrero 2011

71 Find MassSignificant Profiler Professional Pathways Tool Pathway Analysis Find Significant Pathway Is there a significant enrichment of my entities of interest in a particular pathway? Analysis will be performed on every pathway that has been imported into MPP for the matching organism and every pathway created in MPP 15 Febrero 2011

75 Mass Pathway Profiler Analysis Professional using Interaction Database Pathway Analysis Using Interaction Data Base Pathway Analysis in MPP can be used to find relationships between entities of interest. These may be direct interactions or other relationships such as common regulators or common targets. Pathway Analysis utilizes preloaded interaction databases. The information is extracted from literature using Natural Language Processing (NLP) algorithms to search PubMed abstracts. These databases contain details of biological and chemical entities, relationships between entities, and properties of these entities These must be downloaded from the Agilent server and are currently available for the following organisms: Human, Mouse, Rat, Arabidopsis, Drosophila, Yeast, E.coli, Rice, C.elegans, Plasmodium falciparum, Mycobacterium tuberculosis, B. Subtilis, C.reinhardtii, Zea mays, N.crassa The protein sections of these databases are organism specific. All other data is contained in the generic section of the database. 15 Febrero 2011

Brief Introduction to Docking and Virtual Screening with Autodock4 and Autodock Tools Environment set up Launch AutoDock Tools Gui. Aplicaciones --> MGLTools-1.5.4 --> AutoDockTools-1.5.4 You should see

iclef-2002 at Universities of Alicante and Jaen University of Alicante (Spain) ! Introduction! Passage Retrieval Systems! IR-n system! IR-n system at iclef-2002! Conclusions and Future works ! Introduction!

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